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NASA NTRS2020

Kenya Food Security & Agriculture II: Utilizing NASA Earth Observations to Enhance Drought Warning Systems and Develop Capacity to Use the RHEAS Model in Kenya

Twenty-three counties in Kenya experience frequent drought, which damages agricultural productivity and threatens the health and well being of millions. NASA DEVELOP partnered with NASA SERVIR, the Regional Centre for Mapping of Resources for Development (RCMRD) and Kenya’s National Drought Management Authority (NDMA) to enhance drought-detection capacity using NASA Earth observations. Currently, the NDMA publishes monthly Early Warning Bulletins with drought conditions for each arid or semi-arid county in Kenya. These bulletins utilize the Vegetation Condition Index (VCI) from the Moderate Resolution ImagingSpectroradiometer (MODIS) as well as a variety of biophysical, social and economic drought indicators, but do not allow for advanced forecasting. To improve drought-monitoring capabilities, the team created a Combined Drought Indicator (CDI) using the Regional Hydrologic Extremes Assessment System (RHEAS) model and data from Aqua and Terra MODIS and the National Centers for Environmental Prediction. The CDI combined precipitation anomalies, soil moisture anomalies, evaporative stress, and VCI according to weights determined by principal component analysis. To evaluate the performance of the CDI across Kenya, the team compiled a dataset of drought events from historical reports and the NDMA’s records. Results suggested that the CDI detected drought earlier thanVCI alone. However, more validation is needed to ensure that the CDI accurately and consistently detects drought earlier than current warning systems. In order to better understand the behavior of individual indices and the potential for earlier drought detection, the team also conducted a time-lag analysis. The team found that VCI responds to drought, on average, one month later than most other indices included in the CDI, suggesting that incorporating additional indices could improve early drought warning systems in Kenya.

Food Security & Agriculture↗

NASA NTRS2020

Philadelphia Health & Air Quality: Assessing Land Surface Temperature, Vegetation Cover, and Compounding Vulnerability Factors to Identify High Priority Areas for Cooling Initiatives in Philadelphia, Pennsylvania

Heat is the leading cause of weather-related deaths in the US, with heat-related hospitalizations increasing by 2-5% between 2001-2010. In Philadelphia alone, 137 heat-related deaths were recorded between 2010-2018, while a total of 18 daily temperature records have been set since 2010. Temperature is relatively higher in cities compared to rural areas, a phenomenon known as the urban heat island effect.This effect exaggerates daytime maximum temperatures and nighttime heat retention in urban areas, which increases heat exposure inurban environments and especially impacts vulnerable populations. Vulnerability to heat-related illnesses is determined by a combination of risk factors, such as demographics, socioeconomic status, and preexisting health conditions. This project supported the Philadelphia Department of Public Health and Office of Sustainability by identifying priority areas for cooling interventions, such as heat danger educational outreach and urban tree planting. The team developed heat vulnerability scores for each census tract within Philadelphia. Remotely sensed land surface temperature, normalized difference vegetation index, normalized difference built-up index, normalized difference water index, and albedo data were calculated from Aqua Moderate Resolution Imaging Spectroradiometer and Landsat 8 Operational Land Imager/Thermal Infrared Sensor instruments. These variables were weighted against socioeconomic variables and preexisting health conditions using a principal component analysis. A total of 74 census tracts clustered were identified as high-risk areas for heat-related illnesses. 15 of these census tracts also had very low tree density (lower 20th percentile) and should be targeted for tree planting initiatives. The findings of this project will help target interventions to mitigate heat-related health issues and improve the overall wellness of Philadelphia residents.

Health & Air Quality↗

NASA NTRS2020

Kenya Food Security & Agriculture II: Utilizing NASA Earth Observations to Enhance Drought Warning Systems and Develop Capacity to Use the RHEAS Model in Kenya

Twenty-three counties in Kenya experience frequent drought, which damages agricultural productivity and threatens the health and well being of millions. NASA DEVELOP partnered with NASA SERVIR, the Regional Centre for Mapping of Resources for Development (RCMRD) and Kenya’s National Drought Management Authority (NDMA) to enhance drought-detection capacity using NASA Earth observations. Currently, the NDMA publishes monthly Early Warning Bulletins with drought conditions for each arid or semi-arid county in Kenya. These bulletins utilize the Vegetation Condition Index (VCI) from the Moderate Resolution Imaging Spectroradiometer (MODIS) as well as a variety of biophysical, social and economic drought indicators, but do not allow for advanced forecasting. To improve drought-monitoring capabilities, the team created a Combined Drought Indicator (CDI) using the Regional Hydrologic Extremes Assessment System (RHEAS) model and data from Aqua and Terra MODIS and the National Centers for Environmental Prediction.The CDI combined precipitation anomalies, soil moisture anomalies, evaporative stress, and VCI according to weights determined by principal component analysis. To evaluate the performance of the CDI across Kenya, the team compiled a dataset of drought events from historical reports and the NDMA’s records. Results suggested that the CDI detected drought earlier than VCI alone. However, more validation is needed to ensure that the CDI accurately and consistently detects drought earlier than current warning systems. In order to better understand the behavior of individual indices and the potential for earlier drought detection, the team also conducted a time-lag analysis. The team found that VCI responds to drought, on average, one month later than most other indices included in the CDI, suggesting that incorporating additional indices could improve early drought warning systems in Kenya.

Food Security & Agriculture↗

NASA NTRSDate not supplied

Tools for Performing SBG hyperspectral Observing System Simulation Experiment

One of NASA’s Decadal Survey mission, Surface Biology and Geology (SBG), will include a hyperspectral remote sensing imager, which has a very high spatial resolution and a wide spectral coverage (from UV to Near IR). Unprecedented large data volumes will be generated by the SBG hyperspectral instrument. Before the launch of the new satellite, an Observing System Simulation Experiment (OSSE) can be used to study different designs of the new satellite system. One of the key components in an OSSE study is a radiative transfer model (RTM) or forward model. In this presentation, we will describe a Principal Component-based Radiative Transfer Model (PCRTM) which is capable of simulating atmospheric (TOA) radiance or reflectance spectra from far IR to visible and UV spectral regions (50 wavenumber to 30000 wavenumber) quickly and accurately. Multiple scattering from multiple layers of clouds/aerosols are included in the model. The PCRTM has a very good accuracy relative to reference line-by-line radiative transfer models (LBLRTM), and it saves 3-4 orders of magnitude computational time relative to LBLRTM or MODTRAN. The PCRTM model has been successfully used to analyze large volumes of data from hyperspectral sensors such as AIRS, CrIS, and IASI. It has also been used to perform OSSE studies for the Climate Absolute Radiance and Refractivity Observatory (CLARREO) mission. Another useful tool for the OSSE is surface Bidirectional Reflectance Distribution Function (BRDF) database. It is very crucial for the SBG OSSE to include realistic BRDF spectra. Currently, most of the surface reflectance spectra such as those in the ECOSIS and ECOSTRESS are measured at specific observation geometries. We have developed a hyperspectral bidirectional reflectance (HSBR) model which combines Ross-Li BRDF model with the existing reflectance spectral libraries using a principal component analysis. This HSBR model can provide realistic BRDF spectra under various observation conditions. It can also be used to generate realistic BRDF spectra using measurements from multi-band imagers or spectrometers such as MODIS or VIIRS.

Xu Liu↗

NASA NTRSDate not supplied

Novel insights enabled by combining mouse muscle datasets from the Rodent Research-1 mission

Biological space experiments are often expensive and difficult to conduct. As such, it is critical to maximize the value of the data that is collected during these experiments. One way to do this is to combine multiple–previously separate–datasets. This can increase the number of replicates for the conditions of interest (and hence statistical power), allow new multi-factor questions to be asked, and potentially highlight new patterns that otherwise would not have been identified from single-dataset studies. However, the process of combining datasets introduces noise due to inherent technical variations between experiments. To better understand the insights that can be gained from multi-dataset analyses and the problems that may arise from joining multiple datasets, several mouse muscle RNA-Seq datasets from the Rodent Research-1 mission were first selected. Then, using the R package DESeq2, principal component analysis (PCA) plots and differentially expressed gene (DEG) lists between ground and flight muscle samples were generated for individual datasets and for different pairwise combinations of datasets. Several new DEGs were identified in the combined datasets, and patterns in the PCA plots were affected depending on which datasets were joined. Understanding the results of this work will be critical for future studies that seek to perform multi-dataset analyses.

spaceflight↗

NASA NTRS2020

Radiometric approach for the detection of picophytoplankton assemblages across oceanic fronts

Cell abundances of Prochlorococcus, Synechococcus, and autotrophic picoeukaryotes were estimated in surface waters using principal component analysis (PCA) of hyperspectral and multispectral remote-sensing reflectance data. This involved the development of models that employed multilinear correlations between cell abundances across the Atlantic Ocean and a combination of PCA scores and sea surface temperatures. The models retrieve high Prochlorococcus abundances in the Equatorial Convergence Zone and show their numerical dominance in oceanic gyres, with decreases in Prochlorococcus abundances towards temperate waters where Synechococcus flourishes, and an emergence of picoeukaryotes in temperate waters. Fine-scale in-situ sampling across ocean fronts provided a large dynamic range of measurements for the training dataset, which resulted in the successful detection of fine-scale Synechococcus patches. Satellite implementation of the models showed good performance (R(exp 2) > 0.50) when validated against in-situ data from six Atlantic Meridional Transect cruises. The improved relative performance of the hyperspectral models highlights the importance of future high spectral resolution satellite instruments, such as the NASA PACE mission’s Ocean Color Instrument, to extend our spatiotemporal knowledge about ecologically relevant phytoplankton assemblages.

Priscila Kienteca Lange↗

NASA NTRS2020

Version 2 Ozone Monitoring Instrument SO2 Product (OMSO2 V2): New Anthropogenic SO2 Vertical Column Density Dataset

The Ozone Monitoring Instrument (OMI) has been providing global observations of SO2 pollution since 2004. Here we introduce the new anthropogenic SO2 vertical column density (VCD) dataset in the version 2 OMI SO2 product (OMSO2 V2). As with the previous version (OMSO2 V1.3), the new dataset is generated with an algorithm based on principal component analysis of OMI radiances, but features several updates. The most important among those is the use of expanded lookup tables and model a priori profiles to estimate SO2 Jacobians for individual OMI pixels, in order to better characterize pixel-to-pixel variations in SO2 sensitivity, including over snow and ice. Additionally, new data screening and spectral fitting schemes have been implemented to improve the quality of the spectral fit. As compared with the planetary boundary layer SO2 dataset in OMSO2 V1.3, the new dataset has substantially better data quality, especially over areas that are relatively clean or affected by the south Atlantic anomaly. The updated retrievals over snow/ice yield more realistic seasonal changes in SO2 at high latitudes and offer enhanced sensitivity to sources during wintertime. An error analysis has been conducted to assess uncertainties in SO2 VCDs from both the spectral fit and Jacobian calculations. The uncertainties from spectral fitting are reflected in SO2 slant column densities (SCDs) and largely depend on the signal-to-noise ratio of the measured radiances, as implied by the generally smaller SCD uncertainties over clouds or for smaller solar zenith angles. The SCD uncertainties for individual pixels are estimated to be~0.15-0.3 DU (Dobson Units) between ~40°S and ~40°N and to be~0.2-0.5 DU at higher latitudes. The uncertainties from the Jacobians are approximately ~50-100% over polluted areas, and primarily attributed to errors in SO2 a priori profiles and cloud pressures, as well as the lack of explicit treatment for aerosols. Finally, the daily mean and median SCDs over the presumably SO2-free equatorial East Pacific have increased by only~0.0035 DU and ~0.003 DU respectively over the entire 15-year OMI record; while the standard deviation of SCDs has grown by only~0.02 DU or ~10%. Such remarkable long-term stability makes the new dataset particularly suitable for detecting regional changes in SO2 pollution.

OMI, SO2, Remote Sensing↗

NASA NTRS1996

On the Evolution-Dynamics of Tropical Ocean-Atmosphere Annual-Cycle Variability

The structure of ocean-atmosphere annual-cycle variability across the global tropics is extracted from the Comprehensive Ocean-Atmosphere Data Set (COADS) surface winds and SSTs, and oceanic heat-content simulation from a nonlinear shallow water model (forced by COADS wind stress) using the co-variance based rotated principal component analysis technique.

COADS↗

NASA NTRS2019

FIGS: spectral fitting constraints on the star formation history of massive galaxies since the cosmic noon

We constrain the stellar population properties of a sample of 52 massive galaxies – with stellar mass log (M(s)/M(⊙)) ≳ 10.5 – over the redshift range 0.5 < z < 2 by use of observer-frame optical and near-infrared slitless spectra from Hubble Space Telescope’s ACS and WFC3 grisms. The deep exposures (∼100 ks) allow us to target individual spectra of massive galaxies to F160W = 22.5 AB. Our spectral fitting approach uses a set of six base models adapted to the redshift and spectral resolution of each observation, and fits the weights of the base models, including potential dust attenuation, via a Markov Chain Monte Carlo method. Our sample comprises a mixed distribution of quiescent (19) and star-forming galaxies (33). We quantify the width of the age distribution (Δt) that is found to dominate the variance of the retrieved parameters according to principal component analysis. The population parameters follow the expected trend towards older ages with increasing mass, and Δt appears to weakly anticorrelate with stellar mass, suggesting a more efficient star formation at the massive end. As expected, the redshift dependence of the relative stellar age (measured in units of the age of the Universe at the source) in the quiescent sample rejects the hypothesis of a single burst (aka monolithic collapse). Radial colour gradients within each galaxy are also explored, finding a wider scatter in the star-forming subsample, but no conclusive trend with respect to the population parameters.

Ignacio Ferreras↗

NASA NTRS2021

Widely Distributed Exogenic Materials of Varying Compositions and Morphologies on Asteroid (101955) Bennu

Using the multiband imager MapCam on board the OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification, and Security–Regolith Explorer) spacecraft, we identified 77 instances of proposed exogenic materials distributed globally on the surface of the B-type asteroid (101955) Bennu. We identified materials as exogenic on the basis of an absorption near 1 μm that is indicative of anhydrous silicates. The exogenic materials are spatially resolved by the telescopic camera PolyCam. All such materials are brighter than their surroundings, and they are expressed in a variety of morphologies: homogeneous, breccia-like, inclusion-like, and others. Inclusion-like features are the most common. Visible spectrophotometry was obtained for 46 of the 77 locations from MapCam images. Principal component analysis indicates at least two trends: (i) mixing of Bennu's average spectrum with a strong 1-μm band absorption, possibly from pyroxene-rich material, and (ii) mixing with a weak 1-μm band absorption. The end member with a strong 1-μm feature is consistent with Howardite-Eucrite-Diogenite (HED) meteorites, whereas the one showing a weak 1-μm feature may be consistent with HEDs, ordinary chondrites, or carbonaceous chondrites. The variation in the few available near-infrared reflectance spectra strongly suggests varying compositions among the exogenic materials. Thus, Bennu might record the remnants of multiple impacts with different compositions to its parent body, which could have happened in the very early history of the Solar system. Moreover, at least one of the exogenic objects is compositionally different from the exogenic materials found on the similar asteroid (162173) Ryugu, and they suggest different impact tracks.

minor planets↗

NASA NTRS2021

The Dark Side of Pluto

During its departure from Pluto, New Horizons used its LORRI camera to image a portion of Pluto's southern hemisphere that was in a decades-long seasonal winter darkness, but still very faintly illuminated by sunlight reflected by Charon. Recovery of this faint signal was technically challenging. The bright ring of sunlight forward-scattered by haze in the Plutonian atmosphere encircling the nightside hemisphere was severely overexposed, defeating the standard smeared-charge removal required for LORRI images. Reconstruction of the overexposed portions of the raw images, however, allowed adequate corrections to be accomplished. The small solar elongation of Pluto during the departure phase also generated a complex scattered-sunlight background in the images that was three orders of magnitude stronger than the estimated Charon-light flux (the Charon-light flux is similar to the flux of moonlight on Earth a few days before first quarter). A model background image was constructed for each Pluto image based on principal component analysis applied to an ensemble of scattered-sunlight images taken at identical Sun−spacecraft geometry to the Pluto images. The recovered Charon-light image revealed a high-albedo region in the southern hemisphere. We argue that this may be a regional deposit of N2 or CH4 ice. The Charon-light image also shows that the south polar region currently has markedly lower albedo than the north polar region of Pluto, which may reflect the sublimation of N2 ice or the deposition of haze particulates during the recent southern summer.

Pluto↗

NASA NTRSDate not supplied

Reducing OCO-2 regional biases through novel 3D cloud, albedo, and meteorology estimation

This ROSES project tests the addition of novel 3D cloud, albedo fine structure, temperature and water vapor profile to the OCO-2 retrieved system. All new parameters have been added to the ReFRACtor / TROPESS system for testing. Currently, we are comparing 3d-cloud retrievals from OCO-2 radiances to the MODIS-derived EAR3T cloud properties. The water and temperature profile retrievals have been implemented and result in improved XCO2 comparisons to TCCON, and now are implementing principal-component analysis (PCA) to reduce the number of parameters added. We are also studying ECOSTRESS spectral library, AVIRIS-ng, OCO-2 spectral residuals, and albedo retrievals with additional parameters to determine the appropriate characterization of albedo. We find that the current albedo parametrization (2nd order polynomial) is adequate for ocean and vegetation, but not adequate for soil and rock observations.

Reducing OCO-2↗

NASA NTRSDate not supplied

Continuing Global SO2 Data Record from OMI and SNPP/OMPS to JPSS-1/NOAA-20/OMPS

Since 2004, the Ozone Monitoring Instrument (OMI) aboard NASA's Earth Observing System (EOS) Aura spacecraft has been providing global observations that help to constrain the sources, transport, and environmental impacts of anthropogonic and volcanic SO2. The OMI SO2 data record is now being continued with the NASA/NOAA Suomi National Polar-orbiting Partnership (SNPP)/Ozone Mapping and Profiler Suite (OMPS) launched in 2011. Both OMI and SNPP/OMPS SO2 products are produced with the Goddard principal component analysis (PCA) based spectral fitting algorithm. This data-driven technique inherently accounts for various instrumental factors and geophysical interferences, leading to high-quality, consistent SO2 retrievals between OMI and SNPP/OMPS, despite coarser spectral (~0.5 nm vs. ~1 nm) and spatial (13  24 km2 vs. 50  50 km2 at nadir) resolution for the latter. In this presentation, we describe our effort to continue the long-term SO2 climate data record using measurements from the Joint Polar Satellite System (JPSS)-1/NOAA-20 (N20)/OMPS. Launched in 2017, the N20/OMPS is a follow-on for SNPP/OMPS but features a spatial resolution (17  13 km2) that is comparable with OMI. We will discuss our progress implementing the PCA SO2 algorithm with N20/OMPS, especially algorithmic improvements to further reduce retrieval noise and bias for large volcanic eruptions. We will present examples for both continuously emitting sources (e.g., power plants in India and oil/gas fields in the Middle East) and volcanic eruptions (e.g., Raikoke in 2019). We will also compare N20/OMPS SO2 retrievals with OMI and SNPP/OMPS, as well as other instruments such as the ESA Copernicus Sentinel-5 Precursor (S5P)/TROPOspheric Monitoring Instrument (TROPOMI). To assess the ability of N20/OMPS to monitor and quantify SO2 sources, we will run the level 2 retrievals through a top-down emission algorithm to estimate the SO2 emission strengths for a number of point sources. Finally, we will outline our plan for further algorithm refinement and public data release.

SO2↗

NASA NTRSDate not supplied

Variability in Mt. Sharp Group Bedrock as Seen By ChemCam Passive and Active Spectra

The Curiosity rover landed in Gale crater in August 2012 and has since been travelling up the central sedimentary mound known as Mt. Sharp. The ChemCam instrument on Curiosity was designed primarily for the use of Laser Induced Breakdown Spectroscopy (LIBS), where a laser ablates a small amount of material from the target and the spectrum of the resulting plasma yields elemental abundance data. ChemCam’s three spectrometers range from 240-905 nm and can also take passive spectra (without the use of the laser). The spectral range ChemCam passive spectra observe is sensitive to charge-transfer and crystal field absorptions related to iron-bearing minerals. In the first 2934 sols of Curiosity’s mission, 9,400 passive spectra were taken of bedrock targets in Mt. Sharp’s Murray and Carolyn Shoemaker formations. We examine these spectra using spectral slope/ratio and band depth calculations as well as Principal Component Analysis (PCA). For the first time, paired passive spectra and LIBS elemental abundances are compared on a large scale. Finally, CheMin data are compared to ChemCam passive observations to understand sources of spectral variability.

H T Manelski↗

NASA NTRSDate not supplied

Coronado Ecological Conservation: Assessing Vegetation Change Due to Border Wall Construction and Shifting Social Trails

Species monitoring is essential in mitigating the impacts of plant invasion, such as radical changes in an area’s ecosystem, degraded soil health, increased wildfire severity, landslides, and increased flooding. NASA DEVELOP partnered with the National Park Service (NPS) to investigate invasive species in disturbed lands: specifically, areas affected by off-trail walking and US-Mexico border construction activities. The team assessed how construction has impacted the distribution of Lehmann’s lovegrass and Russian thistle invasives throughout Coronado National Memorial, AZ from 1986 to 2022. Using data from Landsat 5 and 8, Sentinel-2, the National Agriculture Imagery Program, and PlanetScope, the team computed vegetation indices including the Normalized Difference Vegetation Index, Normalized Difference Moisture Index, Modified Soil Adjusted Vegetation Index 2, Enhanced Vegetation Index, and Tasseled Cap Wetness, Brightness, and Greenness transformations as vegetation health indicators to input into various machine learning algorithms. To minimize noise, the team conducted Principal Component Analysis on the vegetation indices and spectral bands before running k-means++ clustering and random forest classification algorithms. Between all datasets, we found the median area fully overtaken by invasive plants was 5.37% of the park’s total area in 2022. The NPS will use the end products to help increase restoration efforts in disturbed areas with high concentrations of invasive plants. The NPS’s collection of ground data for 2022–2023, in conjunction with future data collection, will notably improve the accuracy of classification models, leading to more precise monitoring of invasive spread over time.

Carson Schuetze↗

NASA NTRS2023

Optimizing Retrieval Spaces of Bio-Optical Models for Remote Sensing of Ocean Color

We investigated the optimal number of independent parameters required to accurately represent spectral remote sensing reflectances (𝑅 rs ) by performing principal component analysis on quality controlled in situ and synthetic 𝑅 rs data. We found that retrieval algorithms should be able to retrieve no more than four free parameters from 𝑅 rs spectra for most ocean waters. In addition, we evaluated the performance of five different bio-optical models with different numbers of free parameters for the direct inversion of in-water inherent optical properties (IOPs) from in situ and synthetic 𝑅 rs data. The multi-parameter models showed similar performances regardless of the number of parameters. Considering the computational cost associated with larger parameter spaces, we recommend bio-optical models with three free parameters for the use of IOP or joint retrieval algorithms.

Ocean Color↗

NASA NTRSDate not supplied

NASA GeneLab Multi-study Visualization Portal

NASA GeneLab has helped advance the field of Space Biology by providing a public repository where researchers can store, share, analyze and visualize the results of space flight related omics experiments. The GeneLab data visualization portal allows any user, regardless of bioinformatics knowledge or access to computational resources, to interact with the experimental data, draw their own conclusions, and gain insights about the effects of space on living systems. These tools help democratize scientific research and foster the NASA Open Science initiative. The new multi-study feature of the GeneLab visualization platform allows users to mine study metadata from RNA sequencing (RNA-seq) experiments to identify samples of interest by filtering datasets based on organism, tissue, assay technology type, and/or factor. Once samples are selected from multiple datasets, users can combine and normalize the sample data, then utilize the visualization displays, including Principal Component Analysis (PCA) plots, to assess sample distributions. Finally, users can perform differential gene expression analysis on the combined data and visualize the results through PCA plots, Volcano plots, Pair plots, Heatmap, Ideogram and Gene Set Enrichment Analysis. All user-generated results and visualizations will be available for download. Here, we present a biological study using samples from multiple GeneLab RNA-seq datasets and analyzed using the multi-study visualization platform to demonstrate inter- and intra-study variability, as well as commonly differentially expressed genes between spaceflight and ground control conditions across datasets. This new feature opens a wide range of possibilities and opportunities for further development including combining other assay technology types and integration with batch effect correction techniques and machine learning applications. Overall, this tool allows users to increase the statistical power of individual experiments, validate hypothesis, identify patterns, and opens the door to new and exciting research.

space biology↗

NASA NTRSDate not supplied

Batch Effect Correction Methods for NASA GeneLab Transcriptomic Datasets

RNA sequencing (RNA-seq) data from space biology experiments promise to yield invaluable insights into the effects of spaceflight on terrestrial biology. However, sample numbers from each study are low due to limited crew availability, hardware, and space. To increase statistical power, spaceflight RNA-seq datasets from different missions are often aggregated together. However, this can introduce technical variation or "batch effects", often due to differences in sample handling, sample processing, and sequencing platforms. Several computational methods have been developed to correct for technical batch effects, thereby reducing their impact on true biological signals. In this study, we combined 7 mouse liver RNA-seq datasets from NASA GeneLab (part of the NASA Open Science Data Repository) to evaluate several common batch effect correction methods (ComBat and ComBat-seq from the sva R package, and Median Polish, Empirical Bayes, and ANOVA from the MBatch R package). We quantitatively evaluated the ability of these methods to correct for technical batch variables in space biology RNA-seq data using the following criteria: BatchQC, principal component analysis, dispersion separability criterion, log fold change correlation, and differential gene expression analysis. Each batch variable / correction method combination was then assessed using a custom scoring approach to identify the optimal correction method for the combined dataset, by geometrically probing the space of all allowable scoring functions to yield an aggregate volume-based scoring measure. Finally, we describe the way in which the GeneLab multi-study analysis and visualization portal will allow users to examine the presence or absence of batch effects using multiple metrics. If the user chooses to perform batch effect correction, the scoring approach described here can be implemented to identify the optimal correction method to use for their specific combined dataset prior to analysis.

Lauren M. Sanders↗